Crohn's disease (CD) is a debilitating chronic inflammatory bowel disease characterized by patches of inflamed tissue. The underlining cause of inflammation and provocation of the immune response in CD patients has yet to be determined. In theory, the immune system usually reacts against an invading organism such as an insect bite or bacterial infection, or is over-sensitive, as in allergic reactions to grass pollen etc. These reactions cause irritation and pain in the affected area, which subside when the immune system has dealt with the potential threat. Defects in the immune system of CD patients have been reported, both in the ability of the cell to phagocytose and in immune killing after phagocytosis, The cytokine pattern in CD is Th1-like and defect in the ratio of proinflammatory to anti- inflammatory cytokines has been proposed. A specific antigenic stimuli has not been identified, but pathogenic bacteria such as Mycobacterium avium subsp paratuberculosis (MAP) and specific invasive E. coli strains have been proposed. In addition, autoantibodies derived from molecular mimicry from bacterial antigens, or from host origin may also be causative agents of the inflammatory lesions in CD. Defects in the ability of macrophages to present antigen to T-cells and B-cells may also have a role. The mycobacterial theory is based on the significant similarity between CD and Johne's disease, a chronic enteritis in cattle that is caused by MAP. The two diseases share histological and pathological characteristics similar to those in tuberculosis and sarcoidosis. It is believed that MAP may be causing an immune reaction in the gut, resulting in a continuous immune response, which gets better and worse as the number of bacteria increase and decrease. Another possibility is that some parts of MAP like the heat shock proteins similar to parts of the gut lining resulting in triggering an immune response: a process known as autoimmunity. Finally, there may be defects in the immune reaction to MAP or proteins in the gut. In this case, the immune cells fail to deal with the invading organism, which is able to persist in the tissues, causing further inflammation. Many studies have been performed in an attempt to investigate a mycobacterial role in the etiology of CD and its pathogenesis. The outcome has been inconsistent which has added to the controversy. The role of MAP, if any, in the etiology of CD has become increasingly debated in recent years causing a need for clear elucidation. While positive results would change the course of therapy and investigation in CD, a negative result will go a long way toward clearing up the MAP debate. In this study, our team will investigate the overall role of MAP, if any, in CD etiology by addressing the following questions: Is MAP present in CD lesions? Is it culturable? Can MAP be identified using PCR, RT-PCR or fluorescence in situ hybridization (FISH) techniques? Is there any immune reaction activity against MAP in CD patients? Is it cellular, humoral or both? What types of immune cells are present in CD lesions compared to non-inflammatory tissue or tissue from non-IBD and healthy controls? Are there any abnormalities in bacterial phagocytosis by peripheral blood monocytes and neutrophils from CD patients compared to normal cells? Are there factors inhibitory to phagocytosis in CD serum? Are there any abnormalities in antigen presentation and lymphocyte transformation to recall antigens from MAP? Are there any inhibitory or augmenting factors present in the serum from CD patients (cellular and serum crossover)? Our approach in this project is to determine if MAP or reactions against MAP are present in full thickness surgical tissue, heparinized blood and sera specimens from patients with CD using well-developed methodology in the fields of microbiology, immunology and molecular microbiology. We will investigate the presence of MAP in tissue specimens directly by using nested PCR, RT-PCR and FISH and indirectly by culture using a newly developed culture media appropriate for isolation of cell wall deficient form of MAP. We will also investigate the humoral immune reaction in CD sera using p20 antigen, a MAP specific protein. Additionally, the type and state of immune cells will be determined in inflamed versus non-inflamed tissue specimens from CD patients. We will also examine how these cells from CD patient blood are able to ingest and kill MAP, and whether this ingestion results in a normal immune response. This is the first study designed to comprehensively examine the overall presence/absence of MAP in CD tissue and the immune response in CD patients. The results will give us a better idea as to whether MAP causes CD, or whether there is an inherent defect in the immune system, which allows bacterial persistence or autoimmunity to occur in the gut. Ultimately, the outcome of this study will go a long way toward clearing up the MAP debate.